Module 104

General Properties
Below we list the number of gene sets from which the module was composed was originally composed, and the number of genes and experiments that it contains. Clicking on the number of genes will display a detailed list of all the genes in the module. Clicking on the number of experiments will display a detailed list of all the experiments in the module.
Num gene sets:	25
Num genes:	353 (see 756 additional genes for this module)
Num experiments:	493 (116 induced, 377 repressed)
Parent module:	181
Children modules:	41

Gene sets
Below we list the gene sets from which the module was originally composed. Clicking on a gene set will display all the genes associated with that gene set. Also listed are all the other modules in which the gene set participates.
Lessnick02 15
Armstrong01 11
Nutt03 38
Bhattacharjee01 25
Armstrong01 48
Singh02 6
Singh02 12
Lessnick02 25
Singh02 5
Singh02 2
Singh02 3
Armstrong01 12
Nutt03 43
Singh02 20
Singh02 13
Nutt03 36
Singh02 42
Singh02 10
Nutt03 41
Armstrong01 4
Lessnick02 3
Singh02 23
Lessnick02 36
Bhattacharjee01 23
Armstrong01 21

Enriched clinical annotations
For each of the clinical annotations, we tested whether it was enriched in the set of arrays in which the module is significantly induced (or repressed). Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of induced (or repressed) module's arrays in which they appear. We also show the fraction of the module's induced (or repressed) arrays with the given annotation ('Hits (%)' column). For completeness, we also list the total number of relevant induced arrays in the module ('Module hits in category' column), total number of arrays in the compendium in which the corresponding annotation is present ('Arrays in annotation' column), and the total number of relevant arrays in the compendium ('Arrays' column). Note that the 'relevant' arrays may be different for each annotation, since it includes only arrays in which the annotation was relevant (i.e., present or not present) and excludes arrays where the value of the annotation was not known. Rows that correspond to annotations that were enriched in the induced arrays of the module have a red background, while rows corresponding to annotations enriched in the repressed arrays have a green background. For each annotation, we also list the other modules in which it was enriched.
Clinical annotation	Category	P-value	Hits	Hits(%)	Module hits in category	Arrays in annotation	Arrays
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	3.7e-34	135	35.8	377	276	1945
Prostate (Prostate cancer*)	Prostate cancer*	1.0e-32	73	19.3	377	101	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	5.0e-31	109	28.9	377	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	5.0e-31	109	28.9	377	205	1945
Lung cancer (Lung cancer*)	Lung cancer*	4.1e-27	114	30.2	377	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	4.1e-27	114	30.2	377	238	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	2.5e-26	117	31.0	377	252	1945
Cancer (Lung cancer*)	Lung cancer*	2.5e-26	117	31.0	377	252	1945
Prostate (Prostate cancer*)	Prostate cancer*	3.2e-12	27	23.2	116	101	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.9e-08	28	24.1	116	156	1945
Lung carcinoid (Lung cancer)	Lung cancer	5.5e-08	11	42.3	26	20	276
Cancer and cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	6.7e-08	10	2.6	377	10	1945
Cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	6.7e-08	10	2.6	377	10	1945
EWS/FLI expressing fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	6.7e-08	10	2.6	377	10	1945
Fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	6.7e-08	10	2.6	377	10	1945
Skin fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	6.7e-08	10	2.6	377	10	1945
Cancer and cell line (Gliomas*)	Gliomas*	1.6e-07	25	6.6	377	47	1945
Cancer (Gliomas*)	Gliomas*	1.6e-07	25	6.6	377	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	1.6e-07	25	6.6	377	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	1.6e-07	25	6.6	377	47	1945
CNS tumor (Gliomas*)	Gliomas*	1.6e-07	25	6.6	377	47	1945
B cells (Leukemia)	Leukemia	9.5e-07	18	94.7	19	62	141
Liver tissue (Liver cancer*)	Liver cancer*	1.6e-06	28	24.1	116	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	4.8e-06	28	24.1	116	197	1945
Bone marrow (Leukemia)	Leukemia	6.7e-06	11	57.8	19	23	141
Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors)	Neuro tumors	2.2e-05	7	53.8	13	10	90
Lymphoma (B lymphoma)	B lymphoma	7.3e-05	8	100	8	77	245
Acute lymphocytic leukemia (Leukemia)	Leukemia	8.3e-05	21	100	21	99	149
Lymphocytes (Leukemia)	Leukemia	0.0001	19	100	19	91	141

Enriched GO annotations
For each GO annotation, we tested whether it was enriched in the set of genes of the module. Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of the module's genes in which they appear. We also show the fraction of the module's genes with the given GO annotation that are included in this module ('Hits (%)' column). For completeness, we also list the total number of genes in the module ('Module genes' column), total number of genes in the compendium in which the corresponding annotation is present ('Genes in annotation' column), and the total number of genes in the compendium ('Genes' column).
GO annotation	P-value	Hits	Hits(%)	Module genes	Genes in annotation	Genes
fertilization	0.0001	3	1.3	228	3	4566

Visual display

Below is a visual display of the module. Shown are those arrays in which the module's genes significantly change, and the direction of change (induction/repression) in each array is indicated (middle, labeled 'Module changes'; red/green row). The arrays that correspond to the significant clinical attributes are also shown (top; brown rows). The gene sets that compose the module are also shown (left) along with an indication of the membership of the module genes in these gene sets.

You can also view the images within GeneXPress by loading the module gxp file file.

Note: Since there are 493 experiments, this image does not display the individual experiment names, but rather condenses each experiment to a single pixel without displaying its name. You can fully view the image for this module within GeneXPress, by loading any of the four files mentioned in the line above

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